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Since 1926, the fishes in Lake Orta, one of Italy’s deepest natural lakes, were heavily damaged by profundal hypoxia and acidification linked to oxidation of ammonia from industrial effluents and by industrial metal pollution. Of the original 28 fish species, only perch survived the lake’s contamination. Recently, the water quality of the lake has been largely restored by reductions in pollutant inputs, and a massive liming intervention. These interventions restored fish habitat, but it is unclear whether the recent fish reintroductions were successful, and the present status of the fish community is unknown. Here we reviewed the history of the Lake Orta fish assemblage. Using an extensive 2014 sampling campaign, we compared the present fish community to both its pre-pollution composition and to the assemblages of nearby un-polluted, but otherwise similar lakes, Lake Mergozzo and Lake Maggiore. While nearshore fish density now appears normal in lake Orta, the open water community remains impoverished both in numbers and in species. Epilimnetic and hypolimnetic benthic nets were dominated by perch and roach in all the three lakes, but the catch of pelagic nets differed among lakes. Perch (Perca fluviatilis), rudd (Scardinius erythrophthalmus) and brown trout (Salmo trutta) dominated in Lake Orta while shad (Alosa fallax lacustris) and coregonids (Coregonus spp.) were dominant in the open waters of the other two lakes, but missing from Lake Orta. Many fully or partially migratory species, including marble trout (Salmo trutta marmoratus), eel (Anguilla Anguilla) and barbel (Barbus plebejus) were also missing from Lake Orta, a consequence of their initial extirpation and blocked re-colonization routes along the River Strona. In comparison with both pre-pollution and contemporary reference data, the fish community of Lake Orta has not been rehabilitated. The recovery of the littoral community is complete, but cold water species such as burbot (Lota lota), Arctic charr (Salvelinus alpinus) and bullhead (Cottus gobio) are still lacking, as are the pelagic zooplanktivores European whitefish (Coregonus lavaretus) and shad, which dominate offshore communities in the reference lakes, as they did a century ago in Lake Orta. To propose priorities for fish community rehabilitation in Lake Orta, we categorized the conservation, ecological and fishing values of each missing fish species in the lake, and evaluated the cost and probability of success of the needed intervention for each species. This analysis indicated that rehabilitation of shad and European whitefish should receive highest priority.